This article is from the Toys FAQ, by email@example.com (Scott Gordon) with numerous contributions by others.
1) TNG Lt. Cmd. Geordi LaForge (1992) - Originally came with
a removable VISOR before they were permanently attached with
epoxy for safety reasons, card backs also reflect this change.
2) TNG Gowron (1992) - Briefly came with the five pips on his
belt not painted gold.
3) TNG Borg (1992) - Some "reverse negative" Borgs were mistakenly
released with the picture on the card back reversed.
4) TNG Ferengi (1992) - Some Ferengis were released without black
on the boots or a black stripe above the boots.
5) Classic Star Trek Commander Kruge (1995) - Some were mistakenly
released on a card with Kruge card front, but a Spock card back
and a different part number.
6) Star Trek: Voyager Captain Janeway (1995) - It is common to see
Janeway's with a B'elanna Torres trading card instead of the
Janeway trading card.